"Cap" is a slang term for kill, usually with a bullet.
It comes from the ignition cap on the cartridge for a firearm.
"Somebody capped him last night."
"Pop/Bust a cap into somebody" - fire a bullet into them.
"If I find the guy that broke into my house, I'll bust a cap into him."
I'm not sure about some of your examples. In 3, it sounds like "hit" someone, but I'm not familiar with that slang.
1 may refer to psychedelic mushrooms - the piece being the stem and the cap being the top. [But now that I see Peachy's interpretation, his is probably the right interpretation for (1) - sorry]